Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0015439

Physical Location & Seq

Genomic Coordinates Forward (+)

16166231 .. 16168870

Gene Structure 2640 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT5G40400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1833 bp

ATGAAGAATCTCGTTTCAAACCTTCGATTTTTCTCCTCTTATTCTTCTTCGATAGTTCCGCGATGTAGTAACATACCTAAACCAATTCTCAATCCTCTCTACAATTTACTTCCCCAGTCTCAAAACCCTAGTAAAATCGTGGATGTTATCTGTTCAACACTCAACCACAGTGATTATTCCGTCTTGTTACCTAACCTTCGTGACGAGGTGAAATCGCTGATTCCTCATTTGGGTTATCCTGAAATCTCGAGGGTTTTGCTTAGGTTTCAGTCTGATGCTTCTCGAGCTATTACGTTCTTTAAATGGGTTAAATTTGATTTGGGGAAGAGGCCTAATGTTGGTAACTACTGTTTGTTGCTTCACATTCTTGTGTCTTCTAAGAAGTTTCCTTTAGCTATGCAGTTTCTCTGTGAATTGATTGAATTGACATCTAAGAAAGAAGAAGTGGATGTGTTCAGAGTTTTGGTTTCTGCTACTGATGAATGTAATTGGGATCCTGTTGTTTTTGATATGCTTGTGAAAGGTTATCTGAAATTGGGTTTGGTAGAAGAAGGGTTTAGGGTTTTTAGAGAGGTGCTTGATTCCGGTTTTAGTGTTAGTGTTGTTACTTGTAATCATCTACTGAATGGGTTGTTGAAGTTGGATTTGATGGAGGATTGTTGGCAAGTGTATAGTGTGATGTGTAGAGTTGGAATCCATCCCAATACGTATACGTTCAACATTCTTACTAATGTGTTCTGCAACGATTCAAATTTTCGTGAAGTTGATGACTTTTTGGAGAAGATGGAAGAAGAAGGTTTTGAGCCTGATTTGGTTACTTATAATACGTTAGTGAGTAGTTATTGTAGAAGAGGAAGGTTGAAAGAAGCGTTTTATCTGTATAAGATCATGTATAGGCGTCGTGTTGTGCCTGATTTAGTTACTTATACATCGCTTATCAAAGGTCTTTGTAAAGACGGGAGAGTTAGAGAAGCTCATCAGACTTTTCACAGGATGGTAGACAGAGGAATTAAGCCTGATTGCATGTCTTACAATACTCTTATTTATGCTTATTGCAAAGAAGGAATGATGCAACAATCGAAGAAGCTGTTACATGAAATGCTTGGGAATAGCGTTGTTCCCGACAGGTTTACTTGTAAGGTTATAGTTGAAGGATTTGTGAGAGAAGGACGGTTACTTTCTGCTGTTAATTTTGTTGTCGAGCTTAGAAGGTTAAAGGTTGATATCCCATTTGAAGTTTGCGACTTTCTGATAGTAAGTTTATGCCAGGAAGGTAAACCATTTGCAGCAAAGCATCTATTAGATCGAATTATCGAAGAGGAAGGTCACGAGGCTAAACCAGAGACTTACAATAACTTAATTGAGTCTTTGTCCCGTTGTGATGCTATAGAGGAGGCATTGGTTCTAAAAGGCAAACTCAAAAACCAGAATCAAGTACTTGATGCCAAGACATACCGAGCTCTTATAGGCTGCTTGTGTAGGATTGGTAGGAACCGTGAAGCCGAGTCTTTGATGGCAGAAATGTTTGATTCTGAAGTGAAACCGGATTCATTTATATGCGGGGCTTTGGTTTATGGATACTGCAAGGAATTGGATTTCGATAAAGCTGAGAGACTATTGAGTTTGTTTGCTATGGAGTTTAGAATCTTTGACCCAGAGAGTTACAATTCGCTTGTTAAGGCTGTTTGTGAAACGGGATGTGGATATAAGAAAGCGTTAGAGCTTCAAGAAAGAATGCAAAGACTCGGGTTTGTTCCAAACAGGTTAACTTGTAAGTACTTGATCCAAGTGTTGGAACAGCCTTCTTTGCCCAATCATCTGCCTGAGAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0006139 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009451 GO:0009987 GO:0016070 GO:0016787 GO:0016788 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:0090305 GO:0097159 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PPR PPR_1 PPR_2 PPR_3

Protein Analysis

610

Amino Acids

70.19

Weight (kDa)

6.83

Isoelectric Point (pI)

35.37

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	187 - 247	5.5e-08	Pentatricopeptide repeat domain
PPR_2	PF13041	200 - 248	8.7e-14	PPR repeat family
PPR_2	PF13041	244 - 278	9.8e-06	PPR repeat family
PPR_3	PF13812	259 - 314	1.2e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	266 - 297	2.1e-12	PPR repeat
PPR_2	PF13041	269 - 318	1.3e-18	PPR repeat family
PPR	PF01535	272 - 301	3.3e-07	PPR repeat
PPR_3	PF13812	298 - 353	1.3e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	302 - 333	5.8e-12	PPR repeat
PPR_2	PF13041	304 - 348	9.1e-15	PPR repeat family
PPR	PF01535	307 - 337	8.2e-09	PPR repeat
PPR_1	PF12854	335 - 367	6.4e-10	PPR repeat
PPR_2	PF13041	339 - 387	1.2e-10	PPR repeat family
PPR	PF01535	343 - 370	1.4e-06	PPR repeat
PPR_2	PF13041	449 - 494	7.3e-07	PPR repeat family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Orthologous Genes (Group: OG0015439)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G40400 AT5G40400
fragaria_vesca	FvH4_5g31860
malus_domestica	MD09G1028300.v1.1
prunus_persica	Prupe.3G290200_v2.0.a1
pyrus_communis	pycom111g02230
rosa_chinensis	RchiOBHm_Chr2g0173011
rosa_laevigata	RLG00000022149
rosa_multiflora	Rmu_sc0012743.1_g000003
rosa_roxburghii	Rroxscaffold_2G00079320
rosa_samantha	Rh2AG641500 Rh2AG644000 Rh2BG654800 Rh2CG620200 Rh2DG668400
rosa_wichuraiana	Rw2G052920

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	822
AccB7I	CCANNNNNTGG	1 cut(s)	1792
AccI	GTMKAC	2 cut(s)	710, 999
AccII	CGCG	1 cut(s)	61
AciI	CCGC	2 cut(s)	59, 1560
AclWI	GGATC	3 cut(s)	488, 501, 1777
AcsI	RAATTY	2 cut(s)	311, 751
AcuI	CTGAAG	1 cut(s)	1554
AcyI	GRCGYC	1 cut(s)	898
AfaI	GTAC	2 cut(s)	1437, 1778
AfiI	CCNNNNNNNGG	3 cut(s)	230, 338, 1792
AjnI	CCWGG	1 cut(s)	1266
AjuI	GAANNNNNNNTTGG	2 cut(s)	524, 556
AluBI	AGCT	8 cut(s)	287, 395, 974, 1087, 1204, 1460, 1607, 1723
AluI	AGCT	8 cut(s)	287, 395, 974, 1087, 1204, 1460, 1607, 1723
Alw21I	GWGCWC	1 cut(s)	1462
Alw26I	GTCTC	3 cut(s)	123, 1337, 1606
AlwI	GGATC	3 cut(s)	488, 501, 1777
Ama87I	CYCGRG	3 cut(s)	247, 282, 1745
AoxI	GGCC	1 cut(s)	329
ApeKI	GCWGC	2 cut(s)	1286, 1470
ApoI	RAATTY	2 cut(s)	311, 751
AsuHPI	GGTGA	1 cut(s)	220
AvaI	CYCGRG	3 cut(s)	247, 282, 1745
BamHI	GGATCC	1 cut(s)	493
BanII	GRGCYC	1 cut(s)	1462
BarI	GAAGNNNNNNTAC	2 cut(s)	1158, 1190
BauI	CACGAG	1 cut(s)	1328
BbsI	GAAGAC	1 cut(s)	366
Bbv12I	GWGCWC	1 cut(s)	1462
BbvI	GCAGC	2 cut(s)	1298, 1457
BccI	CCATC	5 cut(s)	643, 705, 778, 988, 1507
BcgI	CGANNNNNNTGC	2 cut(s)	238, 272
BciT130I	CCWGG	1 cut(s)	1268
BciVI	GTATCC	1 cut(s)	1571
BcoDI	GTCTC	3 cut(s)	123, 1337, 1606
BfaI	CTAG	1 cut(s)	129
BfmI	CTRYAG	1 cut(s)	1386
BfuI	GTATCC	1 cut(s)	1571
BisI	GCNGC	2 cut(s)	1287, 1471
BlsI	GCNGC	2 cut(s)	1288, 1472
BmcAI	AGTACT	2 cut(s)	1437, 1778
Bme1390I	CCNGG	1 cut(s)	1268
BmeT110I	CYCGRG	3 cut(s)	247, 282, 1745
BmiI	GGNNCC	2 cut(s)	495, 1493
BmrFI	CCNGG	1 cut(s)	1268
BmrI	ACTGGG	1 cut(s)	109
BmsI	GCATC	5 cut(s)	265, 1059, 1303, 1372, 1432
BmuI	ACTGGG	1 cut(s)	109
BpiI	GAAGAC	1 cut(s)	366
Bpu10I	CCTNAGC	1 cut(s)	260
BsaAI	YACGTR	1 cut(s)	708
BsaHI	GRCGYC	1 cut(s)	898
BsaWI	WCCGGW	2 cut(s)	584, 1543
Bsc4I	CCNNNNNNNGG	3 cut(s)	230, 338, 1792
Bse1I	ACTGG	1 cut(s)	115
BseBI	CCWGG	1 cut(s)	1268
BseGI	GGATG	5 cut(s)	148, 454, 697, 999, 1703
BseLI	CCNNNNNNNGG	3 cut(s)	230, 338, 1792
BseMII	CTCAG	2 cut(s)	1599, 1815
BseNI	ACTGG	1 cut(s)	115
BseRI	GAGGAG	2 cut(s)	25, 1406
BseXI	GCAGC	2 cut(s)	1298, 1457
Bsh1236I	CGCG	1 cut(s)	61
BshFI	GGCC	1 cut(s)	331
BsiHKAI	GWGCWC	1 cut(s)	1462
BsiHKCI	CYCGRG	3 cut(s)	247, 282, 1745
BsiSI	CCGG	2 cut(s)	585, 1544
BslFI	GGGAC	1 cut(s)	1357
BslI	CCNNNNNNNGG	3 cut(s)	230, 338, 1792
BsmAI	GTCTC	3 cut(s)	123, 1337, 1606
BsmFI	GGGAC	1 cut(s)	1357
BsmI	GAATGC	1 cut(s)	1740
BsnI	GGCC	1 cut(s)	331
BsoBI	CYCGRG	3 cut(s)	247, 282, 1745
Bsp1286I	GDGCHC	1 cut(s)	1462
Bsp143I	GATC	4 cut(s)	493, 885, 1303, 1782
BspACI	CCGC	2 cut(s)	59, 1560
BspANI	GGCC	1 cut(s)	331
BspCNI	CTCAG	2 cut(s)	1600, 1816
BspFNI	CGCG	1 cut(s)	61
BspLI	GGNNCC	2 cut(s)	495, 1493
BspPI	GGATC	3 cut(s)	488, 501, 1777
BsrI	ACTGG	1 cut(s)	115
BssMI	GATC	4 cut(s)	493, 885, 1303, 1782
BssNAI	GTATAC	1 cut(s)	711
BssNI	GRCGYC	1 cut(s)	898
BssSI	CACGAG	1 cut(s)	1328
Bst1107I	GTATAC	1 cut(s)	711
Bst2BI	CACGAG	1 cut(s)	1328
Bst2UI	CCWGG	1 cut(s)	1268
Bst4CI	ACNGT	4 cut(s)	170, 350, 1173, 1496
Bst6I	CTCTTC	3 cut(s)	320, 844, 1311
BstACI	GRCGYC	1 cut(s)	898
BstBAI	YACGTR	1 cut(s)	708
BstDEI	CTNAG	6 cut(s)	260, 378, 432, 1205, 1608, 1824
BstF5I	GGATG	5 cut(s)	148, 454, 697, 999, 1703
BstFNI	CGCG	1 cut(s)	61
BstKTI	GATC	4 cut(s)	496, 888, 1306, 1785
BstMAI	GTCTC	3 cut(s)	123, 1337, 1606
BstMBI	GATC	4 cut(s)	493, 885, 1303, 1782
BstMWI	GCNNNNNNNGC	2 cut(s)	284, 1807
BstNI	CCWGG	1 cut(s)	1268
BstNSI	RCATGY	1 cut(s)	1027
BstSCI	CCNGG	1 cut(s)	1266
BstSFI	CTRYAG	1 cut(s)	1386
BstSNI	TACGTA	1 cut(s)	708
BstUI	CGCG	1 cut(s)	61
BstV1I	GCAGC	2 cut(s)	1298, 1457
BstV2I	GAAGAC	1 cut(s)	366
BstX2I	RGATCY	1 cut(s)	493
BstYI	RGATCY	1 cut(s)	493
BstZ17I	GTATAC	1 cut(s)	711
BsuI	GTATCC	1 cut(s)	1571
BsuRI	GGCC	1 cut(s)	331
BtgZI	GCGATG	2 cut(s)	76, 915
BtsCI	GGATG	5 cut(s)	148, 454, 697, 999, 1703
BtsIMutI	CAGTG	1 cut(s)	175
CseI	GACGC	1 cut(s)	887
Csp6I	GTAC	2 cut(s)	1436, 1777
CviAII	CATG	3 cut(s)	889, 1024, 1094
CviQI	GTAC	2 cut(s)	1436, 1777
DdeI	CTNAG	6 cut(s)	260, 378, 432, 1205, 1608, 1824
DpnI	GATC	4 cut(s)	495, 887, 1305, 1784
DpnII	GATC	4 cut(s)	493, 885, 1303, 1782
DraI	TTTAAA	1 cut(s)	301
Eam1104I	CTCTTC	3 cut(s)	320, 844, 1311
EarI	CTCTTC	3 cut(s)	320, 844, 1311
Ecl136II	GAGCTC	1 cut(s)	1460
Eco105I	TACGTA	1 cut(s)	708
Eco147I	AGGCCT	1 cut(s)	331
Eco24I	GRGCYC	1 cut(s)	1462
Eco32I	GATATC	1 cut(s)	1225
Eco53kI	GAGCTC	1 cut(s)	1460
Eco57I	CTGAAG	1 cut(s)	1554
Eco88I	CYCGRG	3 cut(s)	247, 282, 1745
EcoICRI	GAGCTC	1 cut(s)	1460
EcoRII	CCWGG	1 cut(s)	1266
EcoRV	GATATC	1 cut(s)	1225
EcoT38I	GRGCYC	1 cut(s)	1462
FaeI	CATG	3 cut(s)	892, 1027, 1097
FaqI	GGGAC	1 cut(s)	1357
FatI	CATG	3 cut(s)	888, 1023, 1093
FauI	CCCGC	1 cut(s)	1553
FblI	GTMKAC	2 cut(s)	710, 999
Fnu4HI	GCNGC	2 cut(s)	1287, 1471
FokI	GGATG	5 cut(s)	155, 461, 684, 1006, 1710
FriOI	GRGCYC	1 cut(s)	1462
Fsp4HI	GCNGC	2 cut(s)	1287, 1471
FspBI	CTAG	1 cut(s)	129
GluI	GCNGC	2 cut(s)	1287, 1471
HaeIII	GGCC	1 cut(s)	331
HapII	CCGG	2 cut(s)	585, 1544
HgaI	GACGC	1 cut(s)	887
Hin1I	GRCGYC	1 cut(s)	898
Hin1II	CATG	3 cut(s)	892, 1027, 1097
HincII	GTYRAC	1 cut(s)	1767
HindII	GTYRAC	1 cut(s)	1767
HpaI	GTTAAC	1 cut(s)	1767
HpaII	CCGG	2 cut(s)	585, 1544
HphI	GGTGA	1 cut(s)	220
Hpy166II	GTNNAC	5 cut(s)	711, 1000, 1131, 1277, 1767
Hpy188I	TCNGA	6 cut(s)	274, 458, 531, 981, 1251, 1534
Hpy188III	TCNNGA	8 cut(s)	200, 239, 247, 282, 758, 1121, 1328, 1727
Hpy8I	GTNNAC	5 cut(s)	711, 1000, 1131, 1277, 1767
Hpy99I	CGWCG	1 cut(s)	903
HpyCH4III	ACNGT	4 cut(s)	170, 350, 1173, 1496
HpyCH4IV	ACGT	4 cut(s)	293, 707, 713, 827
HpyCH4V	TGCA	8 cut(s)	400, 741, 1023, 1056, 1072, 1286, 1584, 1738
HpyF10VI	GCNNNNNNNGC	2 cut(s)	284, 1807
HpyF3I	CTNAG	6 cut(s)	260, 378, 432, 1205, 1608, 1824
HpySE526I	ACGT	4 cut(s)	293, 707, 713, 827
Hsp92I	GRCGYC	1 cut(s)	898
Hsp92II	CATG	3 cut(s)	892, 1027, 1097
KspAI	GTTAAC	1 cut(s)	1767
Kzo9I	GATC	4 cut(s)	493, 885, 1303, 1782
Lsp1109I	GCAGC	2 cut(s)	1298, 1457
LweI	GCATC	5 cut(s)	265, 1059, 1303, 1372, 1432
MaeI	CTAG	1 cut(s)	129
MaeII	ACGT	4 cut(s)	293, 707, 713, 827
MalI	GATC	4 cut(s)	495, 887, 1305, 1784
MboI	GATC	4 cut(s)	493, 885, 1303, 1782
MflI	RGATCY	1 cut(s)	493
MhlI	GDGCHC	1 cut(s)	1462
MlyI	GAGTC	3 cut(s)	1373, 1514, 1737
MmeI	TCCRAC	3 cut(s)	621, 670, 1773
MseI	TTAA	8 cut(s)	300, 309, 1011, 1188, 1214, 1358, 1677, 1766
MslI	CAYNNNNRTG	2 cut(s)	368, 1555
MspI	CCGG	2 cut(s)	585, 1544
MspR9I	CCNGG	1 cut(s)	1268
Mva1269I	GAATGC	1 cut(s)	1740
MvaI	CCWGG	1 cut(s)	1268
MvnI	CGCG	1 cut(s)	61
MwoI	GCNNNNNNNGC	2 cut(s)	284, 1807
NdeII	GATC	4 cut(s)	493, 885, 1303, 1782
NlaIII	CATG	3 cut(s)	892, 1027, 1097
NlaIV	GGNNCC	2 cut(s)	495, 1493
NmeAIII	GCCGAG	1 cut(s)	1528
NmuCI	GTSAC	2 cut(s)	200, 1325
NspI	RCATGY	1 cut(s)	1027
PaeR7I	CTCGAG	2 cut(s)	247, 282
PceI	AGGCCT	1 cut(s)	331
PctI	GAATGC	1 cut(s)	1740
PfeI	GAWTC	9 cut(s)	7, 220, 581, 693, 746, 1429, 1529, 1547, 1644
PflMI	CCANNNNNTGG	1 cut(s)	1792
PkrI	GCNGC	2 cut(s)	1288, 1472
PleI	GAGTC	3 cut(s)	1372, 1513, 1737
PpsI	GAGTC	3 cut(s)	1372, 1513, 1737
Ppu21I	YACGTR	1 cut(s)	708
PsiI	TTATAA	1 cut(s)	822
Psp124BI	GAGCTC	1 cut(s)	1462
Psp6I	CCWGG	1 cut(s)	1266
PspGI	CCWGG	1 cut(s)	1266
PspN4I	GGNNCC	2 cut(s)	495, 1493
PsuI	RGATCY	1 cut(s)	493
RsaI	GTAC	2 cut(s)	1437, 1778
RsaNI	GTAC	2 cut(s)	1436, 1777
RseI	CAYNNNNRTG	2 cut(s)	368, 1555
SacI	GAGCTC	1 cut(s)	1462
SaqAI	TTAA	8 cut(s)	300, 309, 1011, 1188, 1214, 1358, 1677, 1766
SatI	GCNGC	2 cut(s)	1287, 1471
Sau3AI	GATC	4 cut(s)	493, 885, 1303, 1782
ScaI	AGTACT	2 cut(s)	1437, 1778
SchI	GAGTC	3 cut(s)	1373, 1514, 1737
ScrFI	CCNGG	1 cut(s)	1268
SduI	GDGCHC	1 cut(s)	1462
SfaNI	GCATC	5 cut(s)	265, 1059, 1303, 1372, 1432
SfcI	CTRYAG	1 cut(s)	1386
Sfr274I	CTCGAG	2 cut(s)	247, 282
SlaI	CTCGAG	2 cut(s)	247, 282
SmiMI	CAYNNNNRTG	2 cut(s)	368, 1555
SmlI	CTYRAG	2 cut(s)	247, 282
SmoI	CTYRAG	2 cut(s)	247, 282
SnaBI	TACGTA	1 cut(s)	708
SseBI	AGGCCT	1 cut(s)	331
SsiI	CCGC	2 cut(s)	59, 1560
SspMI	CTAG	1 cut(s)	129
SstI	GAGCTC	1 cut(s)	1462
StuI	AGGCCT	1 cut(s)	331
StyD4I	CCNGG	1 cut(s)	1266
TaaI	ACNGT	4 cut(s)	170, 350, 1173, 1496
TaiI	ACGT	4 cut(s)	296, 710, 716, 830
TaqI	TCGA	9 cut(s)	25, 50, 248, 283, 1079, 1200, 1306, 1314, 1599
TatI	WGTACW	2 cut(s)	1435, 1776
TfiI	GAWTC	9 cut(s)	7, 220, 581, 693, 746, 1429, 1529, 1547, 1644
Tru1I	TTAA	8 cut(s)	300, 309, 1011, 1188, 1214, 1358, 1677, 1766
Tru9I	TTAA	8 cut(s)	300, 309, 1011, 1188, 1214, 1358, 1677, 1766
TscAI	CASTG	1 cut(s)	175
TseFI	GTSAC	2 cut(s)	200, 1325
TseI	GCWGC	2 cut(s)	1286, 1470
Tsp45I	GTSAC	2 cut(s)	200, 1325
TspDTI	ATGAA	4 cut(s)	17, 495, 1110, 1539
TspGWI	ACGGA	1 cut(s)	169
TspRI	CASTG	1 cut(s)	175
Van91I	CCANNNNNTGG	1 cut(s)	1792
XapI	RAATTY	2 cut(s)	311, 751
XceI	RCATGY	1 cut(s)	1027
XhoI	CTCGAG	2 cut(s)	247, 282
XmiI	GTMKAC	2 cut(s)	710, 999
XspI	CTAG	1 cut(s)	129
ZrmI	AGTACT	2 cut(s)	1437, 1778

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.